Contents

1 Loading illu1141c.rds

2 Differentially expressed isoforms


Table 1: Glutamatergic matures / Radial glia + Radial progenitors
p_val avg_logFC pct.1 pct.2 p_val_adj cluster geneId transcriptId
Pkm-ENSMUST00000034834.15 0.00e+00 -1.5495424 0.360 0.884 0.0000000 Glutamatergic matures Pkm ENSMUST00000034834.15
Pkm-ENSMUST00000163694.3 0.00e+00 1.3396124 0.831 0.286 0.0000000 Radial glia/precursors Pkm ENSMUST00000163694.3
Clta-ENSMUST00000107849.9 0.00e+00 1.2948718 0.863 0.265 0.0000000 Radial glia/precursors Clta ENSMUST00000107849.9
Clta-ENSMUST00000170241.7 0.00e+00 -0.9428323 0.482 0.873 0.0000000 Glutamatergic matures Clta ENSMUST00000170241.7
Cdc42-ENSMUST00000030417.9 0.00e+00 1.0294242 0.773 0.238 0.0000000 Radial glia/precursors Cdc42 ENSMUST00000030417.9
Cdc42-ENSMUST00000051477.12 3.70e-06 -0.3158706 0.572 0.725 0.1032030 Glutamatergic matures Cdc42 ENSMUST00000051477.12
Tecr-ENSMUST00000165740.8 0.00e+00 0.8471638 0.777 0.370 0.0000000 Radial glia/precursors Tecr ENSMUST00000165740.8
Tecr-ENSMUST00000019382.16 4.42e-05 -0.2651514 0.626 0.788 1.0000000 Glutamatergic matures Tecr ENSMUST00000019382.16
Myl6-ENSMUST00000218127.1 0.00e+00 -0.7690466 0.291 0.635 0.0000000 Glutamatergic matures Myl6 ENSMUST00000218127.1
Myl6-ENSMUST00000164181.1 0.00e+00 0.4205906 0.835 0.667 0.0000002 Radial glia/precursors Myl6 ENSMUST00000164181.1
Myl6-ENSMUST00000219554.1 1.95e-05 0.3239296 0.277 0.116 0.5474868 Radial glia/precursors Myl6 ENSMUST00000219554.1
Dclk1-ENSMUST00000200348.1 1.00e-07 0.4490286 0.612 0.360 0.0014327 Radial glia/precursors Dclk1 ENSMUST00000200348.1
Dclk1-ENSMUST00000167204.7 2.25e-04 -0.3035991 0.201 0.339 1.0000000 Glutamatergic matures Dclk1 ENSMUST00000167204.7


Table 1: Glutamatergic matures / Intermediate progenitors
p_val avg_logFC pct.1 pct.2 p_val_adj cluster geneId transcriptId
Pkm-ENSMUST00000034834.15 0.0000000 -1.5783063 0.360 0.931 0.0000000 Glutamatergic matures Pkm ENSMUST00000034834.15
Pkm-ENSMUST00000163694.3 0.0000000 0.7351223 0.831 0.471 0.0000000 Intermediate progenitors Pkm ENSMUST00000163694.3
Clta-ENSMUST00000107849.9 0.0000000 0.6576249 0.863 0.540 0.0000000 Intermediate progenitors Clta ENSMUST00000107849.9
Clta-ENSMUST00000170241.7 0.0000000 -0.8767158 0.482 0.736 0.0000000 Glutamatergic matures Clta ENSMUST00000170241.7
Myl6-ENSMUST00000218127.1 0.0000000 -0.8498262 0.291 0.609 0.0000001 Glutamatergic matures Myl6 ENSMUST00000218127.1
Myl6-ENSMUST00000164181.1 0.0000013 0.4176744 0.835 0.563 0.0352598 Intermediate progenitors Myl6 ENSMUST00000164181.1
Rpl21-ENSMUST00000035983.11 0.0000000 -0.3455140 0.971 0.989 0.0003371 Glutamatergic matures Rpl21 ENSMUST00000035983.11
Rpl21-ENSMUST00000099272.2 0.0001938 0.2767585 0.288 0.080 1.0000000 Intermediate progenitors Rpl21 ENSMUST00000099272.2
Ogt-ENSMUST00000155792.1 0.0001024 0.4379264 0.594 0.310 1.0000000 Intermediate progenitors Ogt ENSMUST00000155792.1
Ogt-ENSMUST00000150161.7 0.0009047 -0.3585066 0.205 0.356 1.0000000 Glutamatergic matures Ogt ENSMUST00000150161.7
Emc10-ENSMUST00000118808.7 0.0001107 0.4032990 0.655 0.379 1.0000000 Intermediate progenitors Emc10 ENSMUST00000118808.7
Emc10-ENSMUST00000118515.7 0.0003017 -0.4175709 0.374 0.506 1.0000000 Glutamatergic matures Emc10 ENSMUST00000118515.7
Tcf4-ENSMUST00000126946.2 0.0006884 -0.3487926 0.737 0.793 1.0000000 Glutamatergic matures Tcf4 ENSMUST00000126946.2
Tcf4-ENSMUST00000202477.3 0.0016501 0.2800892 0.255 0.092 1.0000000 Intermediate progenitors Tcf4 ENSMUST00000202477.3

Table 1: GABAergic matures / Radial glia + Radial precursors
p_val avg_logFC pct.1 pct.2 p_val_adj cluster geneId transcriptId
Clta-ENSMUST00000107849.9 0.0000000 1.4000766 0.792 0.265 0.0000000 Radial glia/precursors Clta ENSMUST00000107849.9
Clta-ENSMUST00000170241.7 0.0000000 -0.8375791 0.301 0.873 0.0000000 GABAergic matures Clta ENSMUST00000170241.7
Pkm-ENSMUST00000034834.15 0.0000000 -1.0768311 0.387 0.884 0.0000000 GABAergic matures Pkm ENSMUST00000034834.15
Pkm-ENSMUST00000163694.3 0.0000000 1.1588665 0.659 0.286 0.0000000 Radial glia/precursors Pkm ENSMUST00000163694.3
Myl6-ENSMUST00000218127.1 0.0000000 -0.8381279 0.121 0.635 0.0000000 GABAergic matures Myl6 ENSMUST00000218127.1
Myl6-ENSMUST00000164181.1 0.0000000 0.4781358 0.740 0.667 0.0001954 Radial glia/precursors Myl6 ENSMUST00000164181.1
Tecr-ENSMUST00000165740.8 0.0000000 0.9016001 0.595 0.370 0.0000001 Radial glia/precursors Tecr ENSMUST00000165740.8
Tecr-ENSMUST00000019382.16 0.0000000 -0.3962348 0.370 0.788 0.0004211 GABAergic matures Tecr ENSMUST00000019382.16
Snrpa-ENSMUST00000122202.7 0.0000000 -0.2887743 0.092 0.407 0.0000305 GABAergic matures Snrpa ENSMUST00000122202.7
Snrpa-ENSMUST00000126211.1 0.5937879 0.2675566 0.208 0.286 1.0000000 Radial glia/precursors Snrpa ENSMUST00000126211.1
Smarcb1-ENSMUST00000121304.1 0.0000000 -0.3205163 0.121 0.450 0.0000804 GABAergic matures Smarcb1 ENSMUST00000121304.1
Smarcb1-ENSMUST00000000925.9 0.1227085 0.2716136 0.538 0.683 1.0000000 Radial glia/precursors Smarcb1 ENSMUST00000000925.9
Cdc42-ENSMUST00000030417.9 0.0000000 0.8456571 0.434 0.238 0.0009676 Radial glia/precursors Cdc42 ENSMUST00000030417.9
Cdc42-ENSMUST00000051477.12 0.0000689 -0.2704602 0.410 0.725 1.0000000 GABAergic matures Cdc42 ENSMUST00000051477.12

Table 1: GABAergic matures / Intermediate progenitors
p_val avg_logFC pct.1 pct.2 p_val_adj cluster geneId transcriptId
Pkm-ENSMUST00000034834.15 0.0000000 -1.1055950 0.387 0.931 0.0000000 GABAergic matures Pkm ENSMUST00000034834.15
Pkm-ENSMUST00000163694.3 0.0000086 0.5543764 0.659 0.471 0.2411199 Intermediate progenitors Pkm ENSMUST00000163694.3
Myl6-ENSMUST00000218127.1 0.0000000 -0.9189075 0.121 0.609 0.0000000 GABAergic matures Myl6 ENSMUST00000218127.1
Myl6-ENSMUST00000164181.1 0.0000128 0.4752196 0.740 0.563 0.3589580 Intermediate progenitors Myl6 ENSMUST00000164181.1
Emc10-ENSMUST00000118515.7 0.0000000 -0.6523407 0.116 0.506 0.0000023 GABAergic matures Emc10 ENSMUST00000118515.7
Emc10-ENSMUST00000118808.7 0.3169708 0.2939914 0.358 0.379 1.0000000 Intermediate progenitors Emc10 ENSMUST00000118808.7
Clta-ENSMUST00000170241.7 0.0000000 -0.7714626 0.301 0.736 0.0000060 GABAergic matures Clta ENSMUST00000170241.7
Clta-ENSMUST00000107849.9 0.0000000 0.7628298 0.792 0.540 0.0000188 Intermediate progenitors Clta ENSMUST00000107849.9
Tecr-ENSMUST00000165740.8 0.0000002 0.8051937 0.595 0.379 0.0053430 Intermediate progenitors Tecr ENSMUST00000165740.8
Tecr-ENSMUST00000019382.16 0.0052212 -0.2698338 0.370 0.598 1.0000000 GABAergic matures Tecr ENSMUST00000019382.16
Ppdpf-ENSMUST00000138800.7 0.0002458 -0.2980828 0.127 0.345 1.0000000 GABAergic matures Ppdpf ENSMUST00000138800.7
Ppdpf-ENSMUST00000146089.7 0.0190259 0.2732082 0.509 0.437 1.0000000 Intermediate progenitors Ppdpf ENSMUST00000146089.7
Dnaja1-ENSMUST00000030118.9 0.0075899 -0.2504386 0.555 0.805 1.0000000 GABAergic matures Dnaja1 ENSMUST00000030118.9
Dnaja1-ENSMUST00000164233.7 0.1172888 0.3174415 0.324 0.299 1.0000000 Intermediate progenitors Dnaja1 ENSMUST00000164233.7

3 Clta-6exons vs Clta-5exons conserved RNA markers analysis

c(“Glutamatergic matures”,“Glutamatergic imatures”,“Intermediate progenitors”)

## [1] 378
## [1] 54
##          
##           Intermediate progenitors Glutamatergic imatures
##   clta5ex                       31                     16
##   clta6ex                       30                    143
##          
##           Glutamatergic matures
##   clta5ex                     7
##   clta6ex                   205

Table 2: Glutamatergic matures + imatures + Intermediate progenitors
Intermediate progenitors_p_val Intermediate progenitors_avg_logFC Intermediate progenitors_pct.1 Intermediate progenitors_pct.2 Intermediate progenitors_p_val_adj Glutamatergic imatures_p_val Glutamatergic imatures_avg_logFC Glutamatergic imatures_pct.1 Glutamatergic imatures_pct.2 Glutamatergic imatures_p_val_adj Glutamatergic matures_p_val Glutamatergic matures_avg_logFC Glutamatergic matures_pct.1 Glutamatergic matures_pct.2 Glutamatergic matures_p_val_adj max_pval minimump_p_val
Rbfox2 0.0000427 0.7204415 0.900 0.516 0.0033342 0.0716431 0.2740217 0.909 0.875 1 0.0943051 0.2930662 0.941 1.000 1 0.0943051 0.0001282
Khdrbs3 0.0039683 0.3324541 0.367 0.065 0.3095248 0.0867985 0.1770326 0.280 0.062 1 0.2760771 0.1675252 0.400 0.143 1 0.2760771 0.0118576
Celf4 0.0053529 0.5865092 0.733 0.387 0.4175251 0.0953734 0.2797868 0.727 0.500 1 0.3966168 -0.4739896 0.771 0.857 1 0.3966168 0.0159729
Rbfox1 0.0055290 0.3278486 0.500 0.161 0.4312655 0.3039666 0.2480623 0.734 0.562 1 0.4680649 0.1960579 0.761 0.714 1 0.4680649 0.0164956
Khdrbs2 0.0091248 0.3381261 0.267 0.032 0.7117334 0.2069700 0.1566577 0.420 0.250 1 0.5585485 0.1449749 0.741 0.571 1 0.5585485 0.0271253
Rbm8a 0.0330681 -0.2715906 0.800 0.903 1.0000000 0.6470755 0.1084163 0.776 0.750 1 0.4746808 0.1398744 0.888 0.714 1 0.6470755 0.0959601
Srsf9 0.0354839 -0.2473709 0.167 0.419 1.0000000 0.4854427 -0.1230420 0.259 0.312 1 0.2450503 0.1848097 0.380 0.143 1 0.4854427 0.1027192
Rbm17 0.4316580 0.2007831 0.533 0.516 1.0000000 0.0765288 0.2715140 0.643 0.375 1 0.6014612 0.1506773 0.732 0.571 1 0.6014612 0.2124645
Rbm6 0.1007090 0.1927631 0.633 0.419 1.0000000 0.8924127 -0.1230384 0.552 0.500 1 0.2538921 0.2094600 0.644 0.286 1 0.8924127 0.2727215
Tia1 0.1123719 0.2514376 0.900 0.903 1.0000000 0.2212885 -0.2267769 0.881 1.000 1 0.1512979 -0.1568834 0.946 1.000 1 0.2212885 0.3006523
Rbm15b 0.1928203 0.1689013 0.300 0.161 1.0000000 0.2518637 -0.1738750 0.203 0.312 1 0.1273790 0.2229904 0.259 0.000 1 0.2518637 0.3355275
Rbm28 0.1281803 -0.1929628 0.300 0.516 1.0000000 0.2203273 0.2024979 0.343 0.188 1 0.1624234 0.2547265 0.429 0.143 1 0.2203273 0.3373564
Rbm34 0.5512935 0.1048171 0.367 0.323 1.0000000 0.1927078 0.1375243 0.315 0.125 1 0.4963841 0.1028168 0.473 0.286 1 0.5512935 0.4738710
Elavl4 0.3203210 -0.2451712 0.700 0.710 1.0000000 0.2318366 -0.2071666 0.566 0.625 1 0.5864090 -0.1469218 0.522 0.571 1 0.5864090 0.5467260
Rbm25 0.9023799 -0.1263216 0.867 0.968 1.0000000 0.2462796 0.1161778 0.958 0.938 1 0.5791880 0.1482548 0.946 0.857 1 0.9023799 0.5718156
Hnrnpl 0.4183937 0.2082406 0.433 0.387 1.0000000 0.5237274 -0.1226461 0.420 0.438 1 0.3530612 -0.1931463 0.585 0.714 1 0.5237274 0.7292368

c(“GABAergic imatures”,“GABAergic matures”)

## [1] 177
## [1] 49
##          
##           GABAergic imatures GABAergic matures
##   clta5ex                 36                13
##   clta6ex                 56               121

Table 3: GABAergic matures + GABAergic imatures
GABAergic imatures_p_val GABAergic imatures_avg_logFC GABAergic imatures_pct.1 GABAergic imatures_pct.2 GABAergic imatures_p_val_adj GABAergic matures_p_val GABAergic matures_avg_logFC GABAergic matures_pct.1 GABAergic matures_pct.2 GABAergic matures_p_val_adj max_pval minimump_p_val
Rbm8a 0.2069727 -0.1823754 0.679 0.722 1 0.0204891 -0.4961383 0.719 0.769 1 0.2069727 0.0405585
Rbfox3 0.0289644 0.2335917 0.125 0.000 1 0.0870656 0.4921119 0.306 0.077 1 0.0870656 0.0570898
Rbfox1 0.0458238 0.3159214 0.304 0.111 1 0.0920836 -0.1587762 0.182 0.385 1 0.0920836 0.0895477
Rbm28 0.0548879 -0.2773787 0.179 0.333 1 0.4041049 -0.1229073 0.223 0.308 1 0.4041049 0.1067630
Hnrnpa1 0.2411820 0.1061077 1.000 0.972 1 0.0677452 -0.1988541 0.983 1.000 1 0.2411820 0.1309010
Rbm34 0.0767218 -0.2526024 0.179 0.333 1 0.2881425 0.1690053 0.215 0.077 1 0.2881425 0.1475574
Rbm22 0.0804714 0.2399034 0.500 0.306 1 0.1253799 -0.3535297 0.372 0.538 1 0.1253799 0.1544672
Nova2 0.1028911 -0.2290076 0.179 0.333 1 0.4763298 -0.2470994 0.223 0.308 1 0.4763298 0.1951956
Khdrbs1 0.3936772 0.1069216 0.857 0.889 1 0.2568099 0.2009419 0.785 0.692 1 0.3936772 0.4476684
Rbm48 0.4152642 -0.1095102 0.143 0.194 1 0.2956329 0.2299850 0.190 0.077 1 0.4152642 0.5038670
Srsf3 0.4990203 -0.1124026 0.946 1.000 1 0.3246904 0.2329861 0.950 0.846 1 0.4990203 0.5439569
Srsf1 0.3343555 -0.1328446 0.589 0.639 1 0.3547291 0.2763521 0.488 0.385 1 0.3547291 0.5569174
Celf4 0.3456811 -0.1351474 0.768 0.889 1 0.5665273 0.1908124 0.810 0.846 1 0.5665273 0.5718667
Hnrnpl 0.3492847 -0.1867708 0.393 0.444 1 0.6364242 0.1402803 0.331 0.308 1 0.6364242 0.5765697
Srsf11 0.5909726 -0.1034970 0.839 0.806 1 0.4143172 -0.1725061 0.868 1.000 1 0.5909726 0.6569757
Srsf7 0.4759051 -0.1255966 0.750 0.778 1 0.6386502 0.1679206 0.760 0.692 1 0.6386502 0.7253245
Srsf10 0.5093744 0.1439011 0.536 0.472 1 0.4906122 0.2481042 0.496 0.462 1 0.5093744 0.7405240
Rbm10 0.5478488 0.1031773 0.161 0.111 1 0.4954312 0.1486100 0.240 0.154 1 0.5478488 0.7454104

4 Session Info

sessionInfo()
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux buster/sid
## 
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
## 
## locale:
##  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] metap_1.1          cowplot_0.9.4      ggrepel_0.8.0     
##  [4] xtable_1.8-3       knitr_1.21         RColorBrewer_1.1-2
##  [7] forcats_0.4.0      stringr_1.3.1      purrr_0.3.0       
## [10] readr_1.3.1        tidyr_0.8.2        tibble_2.0.1      
## [13] ggplot2_3.1.0      tidyverse_1.2.1    pheatmap_1.0.12   
## [16] dplyr_0.7.8        Seurat_3.0.0.9000  BiocStyle_2.10.0  
## 
## loaded via a namespace (and not attached):
##  [1] Rtsne_0.15          colorspace_1.4-0    ggridges_0.5.1     
##  [4] rstudioapi_0.10     listenv_0.7.0       npsurv_0.4-0       
##  [7] lubridate_1.7.4     xml2_1.2.0          codetools_0.2-16   
## [10] splines_3.5.2       R.methodsS3_1.7.1   lsei_1.2-0         
## [13] jsonlite_1.6        broom_0.5.1         ica_1.0-2          
## [16] cluster_2.0.7-1     png_0.1-7           R.oo_1.22.0        
## [19] BiocManager_1.30.4  compiler_3.5.2      httr_1.4.0         
## [22] backports_1.1.3     assertthat_0.2.0    Matrix_1.2-15      
## [25] lazyeval_0.2.1      cli_1.0.1           htmltools_0.3.6    
## [28] tools_3.5.2         bindrcpp_0.2.2      rsvd_1.0.0         
## [31] igraph_1.2.4        gtable_0.2.0        glue_1.3.0         
## [34] RANN_2.6.1          Rcpp_1.0.0          cellranger_1.1.0   
## [37] gdata_2.18.0        ape_5.3             nlme_3.1-137       
## [40] gbRd_0.4-11         lmtest_0.9-36       xfun_0.4           
## [43] globals_0.12.4      rvest_0.3.2         irlba_2.3.3        
## [46] gtools_3.8.1        future_1.12.0       MASS_7.3-51.1      
## [49] zoo_1.8-4           scales_1.0.0        hms_0.4.2          
## [52] parallel_3.5.2      yaml_2.2.0          reticulate_1.11.1  
## [55] pbapply_1.4-0       stringi_1.2.4       highr_0.7          
## [58] caTools_1.17.1.1    bibtex_0.4.2        Rdpack_0.10-1      
## [61] SDMTools_1.1-221    rlang_0.3.1         pkgconfig_2.0.2    
## [64] bitops_1.0-6        evaluate_0.12       lattice_0.20-38    
## [67] ROCR_1.0-7          bindr_0.1.1         htmlwidgets_1.3    
## [70] labeling_0.3        tidyselect_0.2.5    plyr_1.8.4         
## [73] magrittr_1.5        bookdown_0.9        R6_2.3.0           
## [76] gplots_3.0.1.1      generics_0.0.2      pillar_1.3.1       
## [79] haven_2.1.0         withr_2.1.2         fitdistrplus_1.0-14
## [82] survival_2.43-3     future.apply_1.2.0  tsne_0.1-3         
## [85] modelr_0.1.4        crayon_1.3.4        KernSmooth_2.23-15 
## [88] plotly_4.8.0        rmarkdown_1.11      grid_3.5.2         
## [91] readxl_1.3.1        data.table_1.12.0   digest_0.6.18      
## [94] R.utils_2.8.0       munsell_0.5.0       viridisLite_0.3.0